import re
import copy
import json
+import datetime
import time
from cwltool.process import get_feature, shortname, UnsupportedRequirement
from cwltool.errors import WorkflowException
-from cwltool.draft2tool import revmap_file, CommandLineTool
+from cwltool.command_line_tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
if vwd:
with Perf(metrics, "generatefiles.save_new %s" % self.name):
- vwd.save_new()
+ info = self._get_intermediate_collection_info()
+ vwd.save_new(name=info["name"],
+ ensure_unique_name=True,
+ trash_at=info["trash_at"],
+ properties=info["properties"])
for f, p in generatemapper.items():
if p.type == "File":
if reuse_req:
enable_reuse = reuse_req["enableReuse"]
+ self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
+
try:
with Perf(metrics, "create %s" % self.name):
response = self.arvrunner.api.jobs().create(
find_or_create=enable_reuse
).execute(num_retries=self.arvrunner.num_retries)
- self.arvrunner.processes[response["uuid"]] = self
+ self.uuid = response["uuid"]
+ self.arvrunner.process_submitted(self)
self.update_pipeline_component(response)
logger.info("Creating read permission on job %s: %s",
response["uuid"],
e)
-
- with Perf(metrics, "done %s" % self.name):
- self.done(response)
else:
logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
except Exception as e:
self.output_callback({}, "permanentFail")
def update_pipeline_component(self, record):
- if self.arvrunner.pipeline:
- self.arvrunner.pipeline["components"][self.name] = {"job": record}
- with Perf(metrics, "update_pipeline_component %s" % self.name):
- self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
- uuid=self.arvrunner.pipeline["uuid"],
- body={
- "components": self.arvrunner.pipeline["components"]
- }).execute(num_retries=self.arvrunner.num_retries)
- if self.arvrunner.uuid:
- try:
- job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
- if job:
- components = job["components"]
- components[self.name] = record["uuid"]
- self.arvrunner.api.jobs().update(
- uuid=self.arvrunner.uuid,
+ with self.arvrunner.workflow_eval_lock:
+ if self.arvrunner.pipeline:
+ self.arvrunner.pipeline["components"][self.name] = {"job": record}
+ with Perf(metrics, "update_pipeline_component %s" % self.name):
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
+ uuid=self.arvrunner.pipeline["uuid"],
body={
- "components": components
+ "components": self.arvrunner.pipeline["components"]
}).execute(num_retries=self.arvrunner.num_retries)
- except Exception as e:
- logger.info("Error adding to components: %s", e)
+ if self.arvrunner.uuid:
+ try:
+ job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
+ if job:
+ components = job["components"]
+ components[self.name] = record["uuid"]
+ self.arvrunner.api.jobs().update(
+ uuid=self.arvrunner.uuid,
+ body={
+ "components": components
+ }).execute(num_retries=self.arvrunner.num_retries)
+ except Exception as e:
+ logger.info("Error adding to components: %s", e)
def done(self, record):
try:
processStatus = "permanentFail"
finally:
self.output_callback(outputs, processStatus)
- if record["uuid"] in self.arvrunner.processes:
- del self.arvrunner.processes[record["uuid"]]
+
+ def _get_intermediate_collection_info(self):
+ trash_time = None
+ if self.arvrunner.intermediate_output_ttl > 0:
+ trash_time = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+
+ current_container_uuid = None
+ try:
+ current_container = self.arvrunner.api.containers().current().execute(num_retries=self.arvrunner.num_retries)
+ current_container_uuid = current_container['uuid']
+ except ApiError as e:
+ # Status code 404 just means we're not running in a container.
+ if e.resp.status != 404:
+ logger.info("Getting current container: %s", e)
+ props = {"type": "Intermediate",
+ "container": current_container_uuid}
+
+ return {"name" : "Intermediate collection",
+ "trash_at" : trash_time,
+ "properties" : props}
+
class RunnerJob(Runner):
"""Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
if self.tool.tool["id"].startswith("keep:"):
self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
else:
- packed = packed_workflow(self.arvrunner, self.tool)
+ packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
if self.on_error:
self.job_order["arv:on_error"] = self.on_error
+ if kwargs.get("debug"):
+ self.job_order["arv:debug"] = True
+
return {
"script": "cwl-runner",
"script_version": "master",
}
}
- def run(self, *args, **kwargs):
- job_spec = self.arvados_job_spec(*args, **kwargs)
+ def run(self, **kwargs):
+ job_spec = self.arvados_job_spec(**kwargs)
job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
return
self.uuid = job["uuid"]
- self.arvrunner.processes[self.uuid] = self
-
- if job["state"] in ("Complete", "Failed", "Cancelled"):
- self.done(job)
+ self.arvrunner.process_submitted(self)
class RunnerTemplate(object):
}
def __init__(self, runner, tool, job_order, enable_reuse, uuid,
- submit_runner_ram=0, name=None):
+ submit_runner_ram=0, name=None, merged_map=None):
self.runner = runner
self.tool = tool
self.job = RunnerJob(
output_name=None,
output_tags=None,
submit_runner_ram=submit_runner_ram,
- name=name)
+ name=name,
+ merged_map=merged_map)
self.uuid = uuid
def pipeline_component_spec(self):
projects / arvados.git / blobdiff